rs762583937
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP6
The NM_001849.4(COL6A2):c.1458+9_1458+14del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,612,546 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.000085 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000034 ( 0 hom. )
Consequence
COL6A2
NM_001849.4 intron
NM_001849.4 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.922
Genes affected
COL6A2 (HGNC:2212): (collagen type VI alpha 2 chain) This gene encodes one of the three alpha chains of type VI collagen, a beaded filament collagen found in most connective tissues. The product of this gene contains several domains similar to von Willebrand Factor type A domains. These domains have been shown to bind extracellular matrix proteins, an interaction that explains the importance of this collagen in organizing matrix components. Mutations in this gene are associated with Bethlem myopathy and Ullrich scleroatonic muscular dystrophy. Three transcript variants have been identified for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -1 ACMG points.
BP6
?
Variant 21-46121131-TCAGTGC-T is Benign according to our data. Variant chr21-46121131-TCAGTGC-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 476451.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=1, Likely_benign=1}.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL6A2 | NM_001849.4 | c.1458+9_1458+14del | intron_variant | ENST00000300527.9 | |||
COL6A2 | NM_058174.3 | c.1458+9_1458+14del | intron_variant | ENST00000397763.6 | |||
COL6A2 | NM_058175.3 | c.1458+9_1458+14del | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL6A2 | ENST00000300527.9 | c.1458+9_1458+14del | intron_variant | 1 | NM_001849.4 | P1 | |||
COL6A2 | ENST00000397763.6 | c.1458+9_1458+14del | intron_variant | 5 | NM_058174.3 | ||||
COL6A2 | ENST00000409416.6 | c.1458+9_1458+14del | intron_variant | 5 | |||||
COL6A2 | ENST00000413758.1 | c.81+9_81+14del | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000855 AC: 13AN: 152060Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000283 AC: 7AN: 247336Hom.: 0 AF XY: 0.0000223 AC XY: 3AN XY: 134470
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GnomAD4 exome AF: 0.00000342 AC: 5AN: 1460368Hom.: 0 AF XY: 0.00000551 AC XY: 4AN XY: 726510
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GnomAD4 genome ? AF: 0.0000854 AC: 13AN: 152178Hom.: 0 Cov.: 33 AF XY: 0.0000941 AC XY: 7AN XY: 74408
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Feb 13, 2018 | - - |
Bethlem myopathy 1A Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 27, 2022 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at